Another New Life
by SingleDarkShade
Summary: The TARDIS brings an old friend back onboard to the Doctor's surprise especially as he believes the former companion to be long dead.
1. Chapter 1

Author's Notes: I know I'm meant to be finishing other stories but I have been having a bit of a Doctor Who rewatch and this hit me.

It is finished and will be posted quickly. Not betaed so all errors are mine.

xxx

The TARDIS landed back home within his office at the University and the Doctor leaned against the console.

"So?" he asked.

Bill shrugged, "It was...nice?"

"Nice?" he asked confused, "Is that all you can come up with?"

She shrugged again, "What else do you want?"

Letting out a long sigh the Doctor pushed himself off the console, "Think about it and we'll talk tomorrow."

"Is Bill leaving?" Nardole asked, wandering out from the back of the TARDIS with a few large books.

The Doctor rolled his eyes while Bill opened the door stopping when the TARDIS made a loud clanging noise.

"What was that?" Bill asked worriedly stepping slightly back inside.

The Doctor frowned, "Not sure," he murmured spinning when the door slammed and the TARDIS suddenly went into flight mode.

"What are you doing?" Nardole demanded of the Doctor, the same time the Doctor yelled it at the TARDIS.

"Doctor?" Bill called.

"Just hold on," the Time Lord called to her as the room shook throwing them from side to side.

Finally they slammed to a halt and the Doctor started hitting switches as Bill and Nardole scrambled to his side.

"Where are we?" they asked in unison.

The Doctor grimaced turning the screen to them. Bill gasped as she saw soldiers attacking one man who appeared to be defending people scrambling into a small ship using a sword of all things. Before they could do anything the TARDIS started moving again.

They watched as the man began to appear just inside the doors, sword in his hand blood covering him. The moment he became solid the man took a small step back before he spun to look up at the console.

The Doctor stared pushing Nardole slightly out of the way gasping, "Rory?"

x

Bill watched the man the Doctor had named as Rory take in the room before he looked up at the trio standing at the console once more. His sword came up defensively.

"Rory," the Doctor said holding his hands up walking towards the new arrival, "You're safe. You're in the TARDIS."

"I know where I am," Rory snarled, "What I want to know is where the Doctor is."

Bill glanced at Nardole who winced as the Doctor stopped for a moment. He carefully began to take a few more steps towards Rory who brought his sword up again.

"I am the Doctor," the Doctor stated softly continuing his journey.

Rory frowned at him.

"You know about regeneration," the Doctor reminded the other man, "You know I can change my appearance."

Rory pointed the sword at one of the Doctor's heart, "Doesn't mean you are who you say you are."

Using two fingers the Doctor gently pushed the sword to one side and stepped closer, "I am the Doctor, Rory. I promise."

"Prove it."

Bill heard the plea in those two words, the desperate need for it to be the truth.

The Doctor took one more step forward and smiled, "Fish fingers and custard."

Relief covered Rory's face at the bizarre phrase, the sword clattered to the ground and he closed the gap hugging the Doctor who, to Bill's amazement, hugged him back.

"Nardole," the Doctor called suddenly when the other man became a dead weight against him.

The bald headed assistant quickly ran down to help and between them they lay the now unconscious man on the floor. Bill reached them just as they were resting Rory down and saw he was young, probably not much older than she was. She jumped when the engines started again and stared in astonishment when the unconscious man disappeared.

"What happened?" Bill demanded.

The Doctor sighed, "Medical bay," before he started off through the corridors.

"There's a medical bay?"

x

The Doctor wondered what had happened to his friend as he hurried through the corridors to the Medical Bay. He missed Rory, the compassionate nurse who had reluctantly come onboard with the woman he loved. Rory, who had become a Roman Centurion after being erased from time and remembered two thousand years which haunted him in a way Amy couldn't understand.

He wondered when in Rory's timeline this occurred because the last time he'd seen the other man was just before the Angel threw him back in time. Rory had never mentioned running into one of his future incarnations but the Doctor also knew that the other man could keep a secret if required.

Reaching the Medical Bay he found that the TARDIS had placed Rory on the main bed, the sword sitting on the bench across the room. The Doctor looked down on the patient and checked the scan for any injuries, only half-surprised to find barely a scratch.

"Is he alright?" Bill's voice came from behind him.

The Doctor turned, "Just exhausted."

Nardole appeared with a damp cloth to clean Rory but the moment he touched Rory's face the younger man grabbed Nardole, a dagger appearing from nowhere pressed against Nardole's throat.

"Sir," the cry came as Bill called out.

"Rory," the Doctor moved to him quickly, "It's okay. You're safe. The TARDIS brought you to the med bay. Look around."

Slowly Rory focussed on the room around him and he drew the weapon back from Nardole's throat.

"Doctor?" Rory asked passing the dagger to the Time Lord.

"It's okay, Rory. Do you think you can stay upright to have a shower?" the Doctor asked as the door to the right opened to a shower room.

Rory tilted his head defiantly, "I'm not letting anyone else wash me."

Offering his hand the Doctor helped the other man stand before Rory pulled away and headed to the other room himself.

"Rory," the Doctor called after him, "Nardole will be here if you need any help."

x

The water cascaded down on Rory at the perfect temperature the way it always was making him smile.

The TARDIS had always looked after him.

He'd known from the start that the vessel they travelled in had a personality but after meeting the TARDIS in person he became much more conscientious in the way he treated her. Making sure he tidied up after himself, he would on occasion talk to her and in return she always looked after him.

Grabbing the bottle of shower gel he started to wash the blood away, the blood of the soldiers he had fought to save innocents because no one else would. After five minutes he was clean and after twenty-five more he felt it.

Switching the water off Rory wrapped the large towel around his body drying quickly before pulling on the clothes that were sitting waiting for him. They were his clothes, ones that had been left in the TARDIS when he was thrown back in time.

Rory stood and stared at himself in the mirror wondering where the boy from Leadworth had gone, that innocent kid who just wanted to help people and love the girl with red hair.

He rested his hand on the wall and felt the gentle thrum go through it, "Thank you. I missed you too."

Opening the door Rory found the bald-headed man, Nardole, standing waiting for him.

"The Doctor asks that you join him in his office once you're ready," he said.

Rory frowned slightly, "He has an office in the TARDIS now?"

"Not exactly."

Confused Rory followed the strange man out of the medical bay, reluctantly leaving his sword, and out of the TARDIS into an office where the new version of the Doctor sat waiting for him.

xxx

The Doctor assured Bill that it would be fine, she could leave and he would see her tomorrow. His newest companion hesitated but in the end agreed to leave although she did mutter something about keeping the knives hidden on her way out the door.

After another ten minutes the doors to the TARDIS opened and Nardole led Rory out. The Doctor couldn't help the smile that touched his face seeing Rory before him looking the way he always remembered him. Comfortable denims with a checked shirt, although it did look a little big for him right now, this was Rory once more.

"Nardole, can you get us some tea," the Doctor said as he motioned the seat across from him to the new arrival.

Nardole nodded and disappeared.

Rory sat down and leaned back studying him for several minutes before saying, "At least you don't look twelve anymore."

The Doctor chuckled, "It's good to see you, Rory."

"And you're Scottish," Rory added, "Interesting. So how long has it been since we travelled together?"

"I think you better answer that one first," the Doctor noted.

Rory let out a harsh laugh before answering, "The Angels in New York. Amy and I jumped off a building to kill me so I couldn't be taken but it got me anyway."

The Doctor stared at him confusion covering his face.

"Amy arrived in the past not long afterwards and we lived a good life together," Rory continued, "We adopted a son who married a nice woman and we had grandchildren. One night we went to bed, Amy didn't wake up and then I was sure I had died."

"Rory," the Doctor started when the other man trailed off.

"I woke up, in a coffin, the same age I was the first time I met you. I went travelling for a few years. One day while avoiding UNIT I got sucked through a wormhole and ended up where you found me," Rory finished.

The Doctor stared at him astonished but Nardole choose that moment to arrive with the tea for them. Dismissing Nardole the Doctor quickly poured two cups, automatically fixing Rory's tea the way he liked it making the other man smile that the Doctor remembered.

x

Rory hugged the hot mug to himself watching this new version of his friend watch him over his mug. As he drank Rory began to feel the same comfort he would around the Doctor and found himself asking.

"What am I this time, Doctor?"

"Rory..."

"The last time I was a Nestene Duplicate," he continued, "I seem to keep dying but not dying and I don't understand."

"I wish I had some answers for you," the Doctor replied softly.

Rory pushed his hand through his hair, "How about telling me how you found me because I don't expect that you came looking for me. I wouldn't make that mistake twice."

"The TARDIS brought us to you," the Doctor told him, "She protected you bringing you inside."

Rory smiled slightly.

"She has always liked you," the Doctor chuckled softly.

Rory gave a slight nervous shrug, "That's good to know," he bounced off his chair and moved to the window, "So where and when are we?"

"Bristol University, 2017," the Doctor told him, "But it has been much longer for me since I last saw you and Amy."

Rory's head dropped slightly, exhaustion filling him.

"Why don't you go get some sleep," the Doctor suggested, "We can talk more in the morning."

Rory ran his hand through his hair not sure how to voice his fears.

"The TARDIS will keep you safe," the Doctor read him, "And I promise we won't move from that spot."

Rory smiled in relief, "Thank you, Doctor."

x

The Doctor watched Rory as he headed back into the TARDIS, standing he rested his hand on the box.

"Take care of him," he said smiling as the TARDIS gently hummed in response.

"Sir?"

Turning he found Nardole standing there, "Yes."

"Is he staying?"

"Rory will be here as long as he wants," the Doctor replied, "He is a friend and the TARDIS itself went to rescue him. He is also the father of River Song, so yes he is staying but..."

"Sir?" the question came as the Doctor trailed off for a moment.

The Doctor grimaced, "I want you to go over all the medical data the TARDIS has on Rory. I want to be able to find out what happened to him."

Nardole nodded and disappeared again leaving the Doctor sitting at his desk staring at the picture sitting there.

"I'll look after him, River," he whispered, "I promise."

xxx

To his surprise Rory slept deeply from the moment his head hit the pillow in the room the TARDIS guided him to. Thankfully it wasn't the same one he had shared with Amy.

When he woke the next morning he lay staring at the ceiling wondering what he would do now. Reaching out he placed his hand on the wall, feeling the comforting thrum once more.

"Why did you come and save me?" he whispered to the room, "Why didn't you come before?"

As he expected there was no answer.

Pulling himself out of bed he had a quick shower and dressed in the clothes he found in the wardrobe, more of his own, before he headed to find the kitchen. Opening the door he found the strange bald man cooking breakfast.

"Hi," Rory said softly when the man turned to him, "Nardole, right?"

Nardole nodded.

Rory winced at the silent reply, he took another few steps inside, "I'm sorry about...the...em...the knife to the throat yesterday."

"It's fine," Nardole told him, "Do you want something to eat?"

"Please," Rory smiled slightly.

Taking a seat Rory ate everything put in front of him, amazed how hungry he was.

"The Doctor asked to see you once you're ready," Nardole told him.

Rory nodded, "Sure."

x

"Is it safe?"

The Doctor looked up to find Bill standing in the doorway, "Come in, Bill."

His student walked in and took her usual seat picking up the pen sitting there she idly tapped it off her hand.

"So," Bill said, "Is everything...okay?"

The Doctor chuckled softly, "Yes, everything is fine."

"And the guy with the sword?"

"Rory is getting some rest," the Doctor told her.

Bill leaned back in her seat and frowned, "So, who is he exactly?"

"Rory travelled with me for a while," the Doctor told her.

"Did he come after you with the sword often?" Bill asked receiving a frown.

"Rory Williams is one of the gentlest people you will ever meet," he told her, "The sword is unusual but on occasion he has to pick it up to protect people."

The Doctor stood and started to pace.

"Is he safe then?" Bill asked.

A disapproving frown covered the Doctor's face but before he could say anything the door to the TARDIS opened and Rory appeared.

"Sorry," he said nervously, "Am I interrupting something?"

x

Rory gripped the door of the TARDIS as he looked out into the small office where the Doctor stood with the young woman he recognised from the day before sitting at the desk.

"How do you feel?" the Doctor asked drawing him out of the TARDIS.

Rory nodded softly, "Better."

The Doctor rested his hand on his arm, "Good. I'd like you to meet Bill. I'm tutoring her."

"In what?" Rory couldn't stop himself asking.

Bill chuckled, "It depends what day it is."

Rory smiled offering his hand to her, "I know the feeling. It's nice to meet you."

"And you," Bill replied shaking his hand although he could see she was a little nervous about it.

He grimaced realising this was another apology he needed to give, "Sorry if I scared you yesterday. I honestly don't run around with a sword very often."

"But this was a special occasion?" Bill smiled slightly making him relax a little more.

"It only seems to happen around the Doctor," Rory smiled back flashing his friend an amused look.

"And on that note," the Doctor frowned at him, but Rory could see it was just for show, "We have class. Let's go, Bill."

Bill bounced to her feet before turning back, "Do you want to come?" she asked, "Never know what topic he's going to land on."

Rory shook his head, "Another time. I have some things to do."

"I'll catch up, Bill," the Doctor told her waiting for the young woman to leave before turning to Rory once more, "The TARDIS stored it in its usual place. Get Nardole to give you a key to the office if you feel like going wandering."

With a nod he disappeared leaving Rory alone once more.

Heading back into the TARDIS Rory found the room his sword was kept by the TARDIS, it was still covered in blood and he could see nicks in the steel from the other weapons it had clashed with. Taking a seat he began to clean the weapon before sharpening it once more until it was ready for use once more. Finally finished he placed it back in the case the TARDIS had created for it and put the equipment away once more.

He was safe in the TARDIS with the Doctor and didn't need it attached to him at all times anymore.

He just wondered why she'd saved him and what he would do now.


	2. Chapter 2

Author's Notes: Thanks to everyone who read and reviewed Chapter One.

Enjoy.

* * *

The Doctor was worried.

Rory had barely left the TARDIS in the week since he arrived. The furthest he went was the office where he would drink some tea with the Doctor before he would retreat back to the safety of the blue box.

The Doctor understood that the other man had been lost, alone and forced to become the Last Centurion again which was something Rory hated so he was doing his best to protect himself.

Bill kept trying to persuade him to come to the lectures with them. Rory would politely decline before he would disappear into the TARDIS somewhere.

However he didn't go to the Medical Bay, the place he had always spent his free time. The Doctor was sure that Rory was spending most of his time in the Library but the TARDIS was being very protective of what he was doing.

The TARDIS was also being annoyingly secretive with Rory's medical history only letting Nardole know he was healthy and wouldn't even answer the Doctor's questions concerning the other man.

Finally it was time to step in and get the other man back into the world but he knew there was no point in going to Rory directly – that never worked.

Instead he decided to be sneaky about it.

x

Rory sat in the corner of the library he'd found on his first day back in the TARDIS with one of the larger tomes on the history of a planet called Metadorn. He'd been reading whatever he could get his hands on each day just to give himself something to focus on. He was aware of the looks of concern he was getting from the Doctor but in all honesty he didn't have the energy to deal with it right now.

The good thing about this new version of the Doctor was that he had made a promise to remain on Earth, so Rory didn't have to worry about finding himself on some random planet running for this life, which was why it was such a surprise when he heard the TARDIS engines start up.

Jumping out of his chair Rory ran up to the control room finding the Doctor talking away with Bill on one side and Nardole on the other.

"Where are we going?" Rory demanded.

The Doctor spun, "There you are. I am showing Bill the Caves of Draval, you remember them. I was discussing the effects of the sunset on certain types of crystal so I thought she would like to see it in person."

"I thought you couldn't leave Earth because of your promise," Rory stated folding his arms defensively across his chest.

The Doctor grinned at him, "But this is a time machine, Rory," he bounced around, "I'm sure you remember that. We'll be back moments after we left."

"And you said the TARDIS wouldn't move from that spot," Rory argued.

"For that night," the Doctor replied, "I can't leave her there forever, she gets bored. No one said you had to come with us, you can keep hiding in here like you have been for the past week."

Rory stiffened, "I'm not hiding."

"Then what are you doing, Rory?" the Doctor demanded, "Because it looks a lot like hiding to me."

Anger filled Rory, he saw Bill and Nardole watching before he turned and walked away heading back into the depths of the TARDIS.

"Right, let's go have a look and leave him to sulk," he heard the Doctor say before the door closed.

x

The Doctor ignored Bill and Nardole as they tried to talk to him about Rory while he led them to the caves. His plan to force the other man out of his self-imposed isolation was just beginning and he didn't want them interfering. He knew Rory, he knew how far he could push but if they intervened it would get messy.

There were two versions of Rory, two versions which sometimes warred with one another and that was what made Rory extremely dangerous in many ways. If you got Nurse Williams then it wasn't a problem but the Last Centurion that was a different matter altogether.

It was going to take a delicate balance to pull him back to the world and hopefully get some idea on why he hadn't died with his beloved Amy.

"Come on you two," he called to his current companions, "Let's go."

As they continued to the caves the Doctor mused on his problem.

x

Rory sat in the library his entire body stiff as he fumed.

He should have known not to trust what the Doctor said, should have known it was a lie, should have known...

Rory looked up when the lights dimmed around him slightly, "Fine. I will keep watch over them from the control room. Happy?"

The lights returned to full strength and he sighed. Standing up he headed to the control room, completely different to the one he had known so well during their travels. Despite the change in the room Rory still knew how to work the basic controls so managed to put the view screen on to keep an eye on the Doctor, Nardole and Bill.

Rory folded his arms across his chest again. It had become a familiar stance for him recently which a small voice inside him pointed out was his way to keep the world away from him now.

He continued to observe the other three as they stood at the caves and watched the sunset before they walked back to the TARDIS. Once they were back inside he turned to go but didn't miss the nod from the Doctor before he left the room once more.

* * *

"Why won't you tell me what I need to know?" the Doctor demanded of the TARDIS a week later, "I am trying to help him."

He let out a long sigh as the TARDIS refused to give any information on the other man's medical history other than Rory Williams, healthy.

The one good thing was that Rory had left the safety of the TARDIS a little more in the past few days. He walked to the shops and back yesterday which took over two hours, a current record.

Honestly the Doctor was beginning to get a little worried by the time he returned. Rory simply handed him a bar of Dairy Milk when he passed the Doctor at his desk before he disappeared back into the TARDIS.

"Okay," the Doctor shouted at the control room, "If you don't want to tell me I will speak with the source."

With an annoyed sigh he marched through the TARDIS finding Rory in the library as usual, he still hadn't gone anywhere near the medical bay since the day he'd woken up in it. Pulling a chair over the Doctor took a seat so he was face to face with the other man. Bemused at the sudden presence Rory slowly lowered the book he was reading.

"I'm trying to get the TARDIS to give me information on your medical history," the Doctor stated before Rory can speak, "But she won't give me anything."

"That's odd," Rory said softly.

The Doctor nodded, "She has never refused to give me information before so I am beginning to get concerned."

Rory frowned, a little bemused where this was going.

"I need you to tell me about your family history," the Doctor said, "It will give me somewhere to start."

Rory winced, "It won't."

"Why not?"

"Because I'm adopted," Rory told him with a shrug.

x

Rory watched the Doctor's reaction to the fact he was adopted and there was confusion as well as annoyance in the face Rory was still not quite used to.

"Why do I not know this?" the Doctor demanded, "You and Amy used to give me far too much information on everything and I mean everything."

Rory shrugged, "Because my mum and dad were my mum and dad. I never thought of them as anything else, even when I found out they'd adopted me. They wanted me while whoever actually gave birth to me didn't, so why should I care about them?"

"Okay," the Doctor mused, "I concede on that point but now, considering the fact you're still alive after dying, we need to know who they were."

Rory grimaced but understood, "The thing is I don't know anything. I was found in the church not even a day old. It was my mum who found me," he let out a soft laugh of remembrance, "She used to call me her gift from God. The child she'd never been able to have naturally."

Slightly embarrassed he wiped a tear from his eye, "As far as I know there is absolutely no information on my real parents."

"Then we go back and see who leaves you at the church."

* * *

Leadworth Church was a white stone building in the centre of a well-maintained garden. It was warm and inviting to the people of the village. The blue box which appeared in one corner of the grounds settled for barely a second before two men walked out of it.

"Nardole wasn't happy that we were leaving," Rory noted as they headed to the church.

The Doctor waved his hand, "He spends his life not happy at me."

"And I bet you enjoy pushing those buttons," Rory chuckled.

An innocent look covered the Time Lord's face, "I have no idea what you mean."

Rory rolled his eyes but continued into the church feeling the cool air surround him. He had always liked this building.

It wasn't just that this was where his mother found him and took him in but there was something about the church that was peaceful which had been a counterpoint to his life. To the childhood friends who were loud and bright and exhausting.

A woman was standing at the other end of the aisle fixing flowers and Rory stopped.

"Rory?" the Doctor asked.

Several deep breaths later Rory managed to whisper, "My Mum."

The Doctor caught Rory's shoulder and moved them into the corner, "I know you want to talk to her but you can't. We can't do anything that might stop her finding you...little you..."

"I get it," Rory stopped the other man.

They stood hidden in the corner, Rory letting out a breath he didn't know he was holding when his Mum disappeared into another part of the building. Finally the main doors opened and a woman appeared carrying a baby in carseat.

Rory rested his hand against the wall using it to keep steady, he knew he was here to find out where he had come from but for some reason wasn't prepared for it.

The Doctor absently patted his arm as he watched the woman before gripping Rory's arm tightly.

"What?" Rory demanded.

The Doctor turned to him astonishment written over his face, "Sarah-Jane?"

x

Sarah-Jane Smith checked the note she had ensuring she was at the right place. The baby she was carrying began to fuss slightly and she gently hushed him stroking his soft cheek. He'd been her companion for only a few hours and she was going to miss the little one.

"But you're getting a family," she murmured to him, "Something I can't give you."

Pushing open the doors to the church she smiled at the scent of fresh flowers filling the air, walking further in she looked for the small alcove she was to leave the baby in so he would be found by his new family.

"Sarah-Jane Smith," a voice made her turn to where two men were standing watching her.

One was young with light brown hair he was quite handsome with a Romanesque nose, the other older one with the maddest eyebrows she'd seen he was staring at her in a familiar way.

"Doctor?" she asked softly stunned to see him again.

"This isn't right," he murmured moving towards her, "Because I don't see you again until you're..."

"Older?" Sarah-Jane noted blandly.

He shrugged and it was so Doctor-like there was now no doubt.

"Can I interrupt?" the other man asked, "Doctor, remember why we're here?"

The Doctor turned, "Good point, Rory. Sarah, where did you get the baby?"

Confusion filled her and she offered him the note, "I thought from you."

The Doctor took the note and studied it intently before handing it to the man called Rory. At that moment the baby began to fuss again and the younger man automatically started forward.

"Do not touch that baby, Rory," the Doctor ordered sharply.

Sarah-Jane looked at him confused for a second but she shook her head and concentrated on the child she had been charged with protecting.

"Doctor," Rory said softly.

The Doctor nodded, "Sarah, put the baby where you've been told then come with us."

Nodding she took the little boy and placed him in the small alcove, whispering that he would be safe. Turning to leave him she saw the Doctor motion her over to where he and Rory were hiding.

She reached the hiding spot just as the door near the altar opened. Sarah-Jane watched the woman with long blonde hair walk out with flowers in her arms who stopped hearing the baby cry and the three of them watched as the woman lifted the baby into her arms.

x

Rory felt tears fill his eyes watching his Mum lift the baby version of him into her arms and hold him close. After a moment he turned away, the grief of losing her hitting him once more. A hand rested on his arm and he found the woman who had brought the baby to the church standing there. Without a word she wrapped her arms around him and held him comfortingly, one hand resting on his head, the other rubbing circles on his back.

After a few minutes Rory pulled away and wiped his eyes, "Thank you."

"Not a problem," Sarah-Jane told him, "Now, since the baby is where he is meant to be how about someone explains to me what exactly is going on."

The Doctor nodded, "Let's get to the TARDIS."

Rory felt the Doctor move him from his spot and out of the church. They walked in silence through the gardens and inside the TARDIS once more where Sarah-Jane gave a soft gasp.

"You changed it," she noted.

The Doctor shrugged, "A few times now."

"Okay," Rory interrupted before anything else could be said, "Where did the baby come from? You said you thought it was the Doctor so tell us everything."

"Rory," the Doctor chided softly, "Calm."

His hand twitching to find the sword that wasn't there Rory turned on the Time Lord, "I want to know where I come from. You started this so we are going to find out the answers."

The Doctor caught Rory's face in his hands, "I will but I need Nurse Rory, calm and cool under pressure not Centurion Rory who will stab his way through things."

Shaking slightly Rory pulled back, "Sorry."

Sarah-Jane reached out and squeezed his arm comfortingly, "It's okay. So, Doctor what's going on?"

x

The Doctor quickly explained to his former companion what was happening while Rory sat to one side. It suddenly occurred to the Doctor how little he knew about Rory's family. He knew all about Amy's but whenever it came to a discussion on families, even after meeting Brian Williams, Rory always remained silent.

The information that his mum liked Dusty Springfield had went over his head at the time mostly because he had other concerns but thinking about it, until this moment, it was all the information he had on Rory's mother.

"So where did you get the baby from?" the Doctor turned to Sarah-Jane.

She gave a small shrug, "I was working when I heard the TARDIS. I opened the front door to the cottage and there was the baby asleep in the seat with a note asking me to bring him here at this time."

"Why did you follow the instructions?" Rory asked.

"Because I was sure it was the Doctor who left the child," Sarah-Jane explained.

The Doctor let out a long hum of thought.

"What?" Rory demanded.

The Doctor turned and handed the note to Rory again, "I wrote it."

"Of course you did," Rory snapped getting annoyed again before stopping, "Wait, what does that mean?"

"It means that sometime in the future I find you," the Doctor told him.

Snatching the note back the Doctor opened a panel on the TARDIS console and placed the letter in it.

"What are you doing?" Rory and Sarah-Jane asked in unison.

"Checking for hidden messages," the Doctor replied as he bounced about hitting switches, "Because if I sent it then I need to be able to send it so there has to be information to let me."

Rory turned to Sarah-Jane, "This is why I spend most of my time with a headache."

"I remember the feeling," she replied with a slight smile.

Before the Doctor could retort the TARDIS beeped making all turn, "I have co-ordinates."

"And I have to leave," Sarah-Jane told them.

"Why?" Rory asked.

She smiled up at him, "Because I can tell I shouldn't be here."

The Doctor beamed at her, "My brilliant Sarah-Jane. I will see you again and you will be amazing the way you always are."

She gave him another smile before wrapping her arms around the Doctor, "Take care of him, Doctor. I can see how lost he is."

"I'm doing my best," the Doctor murmured in her ear, "Just look after yourself."

When they parted Sarah-Jane turned to Rory and hugged him as well before she walked out the TARDIS without looking back.

* * *

Final Note: This does completely ignore the facts given in Dinosaurs On A Spaceship regarding Rory and his Dad but let's just not mention that.

The third and final part will be up soon.


	3. Chapter 3

Author's Note: This is the final chapter, hope you enjoy.

* * *

Rory gripped the railing as the TARDIS flung them from side to side while heading to the co-ordinates the Doctor had entered. Finally they landed and he looked over at the Time Lord.

"Where are we?" Rory asked.

The Doctor shrugged, "No idea. Let's find out."

Rory dropped his head, "Why not check before we go out," he held up his hand, "Don't tell me. That wouldn't be any fun."

The Doctor grinned, "You remember."

Rolling his eyes Rory followed the Time Lord out of TARDIS and into a white corridor. The Doctor walked one way and then another before frowning, licking his finger and holding it in the air for several minutes.

"You have no idea where we are," Rory leaned against the wall beside the TARDIS, "Do you?"

"I'm working on it," the Doctor told him.

Rory chuckled, "Well we're in space."

"How do you know that?" the Doctor asked, surprise and irritation in his voice.

With an amused smile Rory pointed just behind the TARDIS, "Because I can see out the window."

He clearly heard the Doctor swear at him under his breath before stalking off in a random direction. Chuckling to himself Rory followed on.

x

The Doctor could taste something odd about the air in the ship/space station they'd materialised onboard. He was beginning to get a very bad feeling about this.

"Doctor?" Rory's whispered call made him pause for a moment. He turned and held up a finger to get him to be quiet.

"I hear voices," the Doctor murmured softly, "Stay completely quiet we don't want anyone else knowing we're here."

"I remember the drill," Rory replied before adding, "So make sure you don't sneeze."

The Doctor rolled his eyes but didn't reply instead moved closer to the doors at the end of the corridor. Using the sonic screwdriver he opened the doors just enough so they could see and hear inside.

"Please," a woman cried distraught, "Please don't take my baby away."

The familiar laugh sent a shiver along the Doctor's spine, "It's not your baby, my dear. He is my experiment and I must admit he came out better than I expected."

The Doctor felt Rory stiffen at his side but he managed to remain silent.

"Don't take him," the woman cried, "I will do anything."

"You will but that won't do anything to change my mind," the other occupant replied, "I am however feeling magnanimous today because of how well the experiment went I will let you have a few minutes with him."

x

"Come on, Rory," the Doctor pulled his arm the moment the other man left the room via the door at the other side, "Help the woman, do not touch the baby."

The woman was standing over a crib turning when she heard them and Rory saw the fear in her eyes.

"I'm the Doctor, this is Rory," the Time Lord quickly introduced, "We're here to help."

Rory's brain caught up with what was happening and he realised suddenly that the frightened woman was his real mother.

"Rory," the Doctor stated deliberately, "Help her to the TARDIS while I take the baby."

Nodding he slipped his arm around the woman's waist and started them moving, seeing the Doctor gently lift the child from the cot. Rory kept his focus on the woman, barely more than a girl really she looked about ages with Amy when the Doctor came back the first time.

"We're almost there," Rory assured her as they continued to the blue box.

He blinked when the Doctor clicked his fingers and the doors opened but didn't have time to think it over. Once inside Rory moved to the console, still holding the woman, waiting for the Doctor. As soon as the Doctor stepped inside, slamming the door behind him, Rory hit the button to take them home.

"Please," the woman whispered reaching for the baby.

The Doctor shook his head, "First, Rory is going to take you to the medical bay and make sure you're healthy," he held up his hand to stop her saying anything else, "Don't worry, the little one will be there while I make sure he's okay."

Rory nodded when the Doctor motioned him to go and guided the woman to the medical bay.

x

"What's your name?" Rory asked gently, helping her onto the bed.

"Lily," she whispered, her eyes darting to where the Doctor had placed the baby.

Rory smiled down at her, for the first time taking in her appearance and seeing a lot of himself in her face. Her eyes and her sandy brown hair were the same as his and he recognised the confused quirk of her lips.

"I'm Rory," he told her, "You don't have to worry, I'm a nurse. I just want to make you're okay."

She nodded turning sharply when the baby gave a cry.

"Yes, I know it was cold," the Doctor said to the child, "But I have to listen to your heart."

Lily turned to Rory confused who shook his head, "It's easier not to ask."

She gave a small laugh and Rory felt his heart clench slightly wondering how long he would get to spend with her. Quickly Rory gave her a check-up finding she was completely healthy.

"Doctor?" he turned to the Time Lord.

The man in question lifted the baby once more and rested the child in his mother's arms, "He's healthy."

"But different," Lily whispered hugging the baby close.

The Doctor nodded before finishing, "And I am sorry, Lily, I am so sorry but you can't keep him and I can't give you much time with him either."

"No," Lily cried.

The Doctor sighed, "I wish you could raise that little boy but you know that the man who did this will find you and when he does..." he trailed off, "This is the only way to protect that little boy."

Lily nodded, rocking the child as she tried not to cry.

"Doctor," Rory said, "Can't we..."

"No," the Doctor cut him off, "The baby was barely a day old when found remember and we need to get him to that rendezvous."

"But..."

"I will explain everything once we do this," the Doctor promised.

x

Rory felt ill as he watched Lily hold her child close, hold him close knowing she would never see her baby again. It was beginning to look like a family trait and he was beginning to understand how River felt when she saw them before they knew who she was.

"You need to remember that I always love you," Lily whispered to the baby, "And I know you'll be a good man when you grow up."

Feeling tears prick his eyes Rory turned away, focussing on the Doctor writing his note for them to find earlier today.

"Okay," the Doctor appeared carrying the car seat and moved to Lily, "We'll be landing in a few minutes. You have to say goodbye."

Lily was crying at this point but placed her baby in the seat whispering how much she loved him over and over. When the Doctor lifted the seat Lily gently kissed her son's forehead once more before staggering away. Automatically Rory caught her and wrapped his arms around Lily while she cried on his shoulder. He continued to comfort his real mother while the Doctor left the baby on Sarah-Jane's doorstep.

When the Doctor reappeared he went straight to the console and hit a few buttons before turning back to them.

"I think it's time we all had a conversation," he said.

x

The Doctor placed a mug of tea in front of Lily while Rory took his own, they'd relocated to his office and the chairs sat in a small circle for this discussion. The new knowledge of Rory's true origins was staggering but he had to deal with the young woman first.

"You seemed unfazed by travelling in the TARDIS," the Doctor noted, "So, why don't you tell us where you're from originally."

"My name is Lily Thomas," she introduced herself holding her mug tightly, "I work for UNIT."

"When?" Rory asked.

Lily shrugged, "It was 1973 when I was taken by that man."

"Do you know who the man was?" the Doctor asked.

Lily nodded.

"Who was he?" Rory asked getting a sharp glance from the Doctor.

"He called himself the Master," Lily shuddered, "Claimed he was a Time Lord, just like you, Doctor."

The Doctor nodded.

Lily took a deep breath, "He told me he wanted to perform a small experiment, to create a half-human child for something. He extracted my eggs then a few weeks later implanted them in me so I would carry the ones that were viable."

Rory looked at the Doctor visibly shaken.

"How many children did you have, Lily?" the Doctor asked.

Lily wiped her eyes, "Just one," she took in a shuddering breath, "What happens to my baby? Please tell me he is safe."

"Tell her," Rory pleaded.

The Doctor nodded softly, "Lily, your son was taken in by two wonderful people who raised him to be caring and compassionate. He became a nurse, met a girl he adored and married her."

Lily smiled holding back tears.

"And he's sitting at your side," the Doctor finished.

Lily spun to look at Rory who smiled at her, "Hi."

* * *

The Doctor left Rory and Lily to talk for as long as he could while he programmed the TARDIS to protect Rory's history. She had already done this but if he didn't give the instruction it would cause problems later on.

He checked the clock.

There was only a short time he could allow them to spend together before he had to separate them for their safety. Once that was done then he would study the files he'd stolen and discover exactly what the Master had done and what that meant for Rory.

Although he gave them every second he could the Doctor knew they had run out of time. He left the TARDIS finding mother and son hugging.

"I'm sorry," he interrupted them, "But Lily, it's time."

Taking a deep breath she pulled back and studied Rory's face for a moment, "I could never have imagined how wonderful you would turn out to be and I am so sorry I had to leave you. I will always love you, Rory. My son."

Rory smiled softly, "I love you too, Mum."

With a final embrace she walked into the TARDIS without looking back.

x

"Tell me something," Lily said as she leaned against the rail.

The Doctor looked over at his guest as he piloted the TARDIS back to UNIT in 1973, "If I can."

"Will you look after Rory?" she asked.

The Doctor smiled at her, "I have and will always look after him, Lily. I promise. He is my family."

She wiped her eyes and shuddered, "I was so scared. Alone and suddenly pregnant but then...oh then there he was so beautiful. I know I can never see him again but make sure he knows I want to. Make sure he knows that I will always love him."

The Doctor moved to her side and rested his hand on her arm, "He knows."

Without another word he opened the doors to the TARDIS and stepped out finding the welcoming committee waiting for them looking bemused.

"Brigadier," he greeted the man with a grin, "I don't have time to go over this. I'm sure you know Lily Thomas. She'll tell you what happened but unless I mention it first don't speak about anything she tells you to me. Or anyone else."

"Doctor?" the man asked confused.

"I can't stay," he stopped the other man from speaking, "Lily will explain everything."

Without giving anyone else a chance to say anything he jumped back into the TARDIS and headed back to check on Rory.

x

Rory sat watching the TARDIS disappear then reappear within two minutes knowing he'd never see his birthmother again, the same way he would never see the mother that raised him.

He'd told her his story, well a sanitised happier version without the random de-aging and multiple deaths.

"I've returned her to her own time," the Doctor said the moment he stepped out the blue box, "UNIT will look after her."

Rory looked up at him, "Thank you."

The Doctor nodded, "Now we have to investigate what your non-human side is."

"I don't think I want to know," Rory whispered.

"I understand," the Doctor told him, "But considering this was done by the Master then I need to know. I need to make sure I can keep my promise to the women who love you."

Rory stood and pushed a hand through his hair, "Tell me when you find it. I need to get some air."

The Doctor nodded and Rory headed out the office down the stairs then went for a walk around the University.

* * *

"Should I ask or should I just find something that will actually get you drunk?"

The Doctor looked up to find Nardole standing there watching him, "I'd take the drink but right now I need to be completely conscious."

Nardole frowned, "Is it that bad?"

"It's..." he hesitated, "Concerning. When he had no idea that he wasn't fully human Rory was safe but now he has the knowledge..."

"He can't leave," Nardole noted with a grimace.

The Doctor nodded, "The TARDIS is the safest place for him to be and I don't know if he'll accept that."

"Are you going to tell him what you found?"

"I'm not sure," the Doctor sighed, "I should but telling him is adding another alarm in his psyche and not telling him could push him away from the safest place there is."

Nardole sat down and leaned back in the chair, "She told me about him once."

"Who?"

Nardole rolled his eyes, "River Song, who else. She told me about her father one night, about how incredible he was. Do you want to know the one thing I took from the story?"

"What was that?"

"That he was her hero," Nardole said, "That her father was someone who would do what was best."

The Doctor smiled slightly, "Thank you, Nardole."

With a nod he stood and left the room once more before calling back, "I'll have tea ready for when you talk with him."

x

"How was your walk?"

Rory held up the bag he was carrying, "I picked up some more Jammie Dodgers," he said before taking his seat and a deep breath, "What did you find?"

"If I said that I can't tell you," the Doctor asked, "In order to protect you, would you accept that?"

Rory stared at him, his eyes showing that he was going over everything in his head. He finally looked up and asked, "If I said I want to know will you tell me?"

"Yes."

"Then I trust that you're keeping this from me for a very good reason," Rory told him.

The Doctor stared at him surprise clearly on his face.

Rory chuckled slightly at the other man, "You always focussed on Amy, Doctor. You forgot me sometimes and you still forget how much I pay attention. You do things to help the people you care about and I know, even if it took me some time to realise it, you do care about what happens to me."

The Doctor stood and walked around the room for a few moments before turning back to Rory.

"Just now the best thing I can do is keep this information from you," the Doctor told him, "I promise that as soon as I am able to I will tell you everything you need to know."

Rory nodded, "Thank you."

"You should be fine to resume a life here," the Doctor told him, "Find a job, go to the movies and whatever else you humans like to do."

Rory looked at him with a slight grimace, "Are you kicking me out?"

"Never," the Time Lord replied, "The TARDIS itself came for you, she chooses the people she wants to keep onboard and she has always liked you."

A slight smile touched Rory's lips, "Amy used to complain about that."

"So do I sometimes," the Doctor threw in.

"I think I'd like to stick around here for a while," Rory told him, "I have some money, Amy and I opened some savings accounts which I can access just in case we needed them. We were never sure if we would manage to find a way through time so wanted to be prepared."

The Doctor smiled and offered his hand, "Welcome home, Rory Williams."

Rory took the other man's hand shaking it feeling for the first time since he'd lost Amy he had a home again.


End file.
